Contacts of the helix formed by residues 930 - 937 (chain B) in PDB entry 3KKA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 930 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922B LEU* 4.3 1.8 - - + -
927B MET* 3.1 29.0 + - + +
928B LYS 2.9 2.0 + - - -
929B ARG* 1.3 93.8 - - + +
931B ILE* 1.3 66.8 + - - +
932B LEU 3.3 2.5 - - - -
933B HIS* 3.1 40.9 + + - +
934B PHE* 3.1 22.6 + - + -
957B GLY 4.7 2.9 - - - -
958B ILE* 3.7 43.8 - - + +
959B THR 5.4 0.2 + - - -
960B LEU* 4.0 12.0 - - - +
963B HIS* 2.6 47.1 + + + +
967B ILE* 4.4 7.9 - - + -
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Residues in contact with ILE 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918B VAL* 4.0 17.5 - - + -
919B SER* 4.2 23.6 - - - +
922B LEU* 4.0 21.0 - - + +
928B LYS* 3.0 30.2 + - + +
929B ARG 3.4 2.4 - - - +
930B TYR* 1.3 75.9 - - - +
932B LEU* 1.3 70.0 + - + +
934B PHE* 3.1 5.2 + - + +
935B HIS* 3.0 28.0 + - + +
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Residues in contact with LEU 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B ARG 5.0 2.1 + - - +
930B TYR 3.3 0.6 - - - -
931B ILE* 1.3 81.5 - - + +
933B HIS* 1.3 62.0 + - + +
935B HIS* 3.1 26.6 + - + +
936B SER* 2.7 48.1 + - - +
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Residues in contact with HIS 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B ARG 4.0 10.2 + - - -
930B TYR* 3.1 44.4 + + - +
932B LEU* 1.3 79.6 + - + +
934B PHE* 1.3 61.9 + - - +
936B SER* 3.4 7.3 + - - -
937B ALA* 3.1 23.7 + - - +
956B MET* 3.2 33.9 - - + +
957B GLY* 4.2 9.1 + - - -
958B ILE* 4.1 17.0 - - + -
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Residues in contact with PHE 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918B VAL* 4.1 15.0 - - + -
921B TRP* 3.5 35.4 - + - -
922B LEU* 4.0 19.7 - - + -
930B TYR* 3.1 20.5 + - + -
931B ILE* 3.1 9.6 + - + +
933B HIS* 1.3 73.9 - - - +
935B HIS* 1.3 64.4 + - - +
937B ALA 3.3 1.9 + - - -
938B GLY 3.2 3.3 + - - -
939B LEU* 2.8 54.8 + - + +
945B VAL* 4.0 6.1 - - + -
948B LEU* 3.7 26.5 - - + -
953B LEU* 4.3 8.5 - - + -
956B MET* 3.7 16.8 - - + -
958B ILE* 3.7 20.9 - - + -
967B ILE* 4.4 5.4 - - + -
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Residues in contact with HIS 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931B ILE* 3.0 16.0 + - + +
932B LEU* 3.3 29.8 - - + +
934B PHE* 1.3 74.6 - - - +
936B SER* 1.3 59.7 + - - +
938B GLY* 2.9 20.6 + - - -
939B LEU 4.3 0.4 + - - -
940B ASP* 3.3 29.3 + - - +
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Residues in contact with SER 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932B LEU* 2.7 33.7 + - - +
933B HIS* 3.6 8.2 - - - -
934B PHE 3.2 0.2 - - - -
935B HIS* 1.3 75.6 - - - +
937B ALA* 1.3 60.2 + - - +
938B GLY 3.1 1.1 + - - -
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Residues in contact with ALA 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B HIS 3.1 16.0 + - - +
934B PHE 3.3 1.9 + - - +
936B SER* 1.3 76.2 - - - +
938B GLY* 1.3 60.1 + - - +
939B LEU* 3.5 31.9 + - + +
956B MET* 3.9 19.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il